Commit fca93af0 authored by Yakubov, Sergey's avatar Yakubov, Sergey
Browse files

Merge branch '76-proper-fail-job-on-object-store-error' into 'dev' 

Resolve "Proper fail job on object store error"

Closes #76

See merge request !61
parents dd6bfeae 6518668b

.gitlab-ci.yml

+2 −2
Original line number Diff line number Diff line
@@ -9,8 +9,8 @@ variables: 
  CONTAINER_GALAXY_URL: "${CI_REGISTRY_IMAGE}"

  CONTAINER_GALAXY_BASE_URL: "${CONTAINER_GALAXY_URL}/base"

  CONTAINER_GALAXY_COMMIT_URL: "${CONTAINER_GALAXY_URL}/commit"

  GALAXY_VERSION_PYTHON: 23.1.dev0+ornl

  GALAXY_VERSION_DOCKER: 23.1.dev0.ornl

  GALAXY_VERSION_PYTHON: 23.1.dev1+ornl

  GALAXY_VERSION_DOCKER: 23.1.dev1.ornl



# This import is for the func_rse_docker_* functions

before_script:

lib/galaxy/jobs/__init__.py

+2 −0
Original line number Diff line number Diff line
@@ -1971,6 +1971,8 @@ class MinimalJobWrapper(HasResourceParameters): 
                log.debug("(%s) setting dataset %s state to ERROR", job.id, dataset_assoc.dataset.dataset.id)

                # TODO: This is where the state is being set to error. Change it!

                dataset_assoc.dataset.dataset.state = model.Dataset.states.ERROR

                dataset_assoc.dataset.update_time = datetime.datetime.now()



                # Pause any dependent jobs (and those jobs' outputs)

                for dep_job_assoc in dataset_assoc.dataset.dependent_jobs:

                    self.pause(

lib/galaxy/objectstore/rucio.py

+1 −0
Original line number Diff line number Diff line
@@ -365,6 +365,7 @@ class RucioBroker: 
                        "force_scheme": rse_scheme["scheme"],

                        "rse": rse_scheme["rse"],

                        "base_dir": base_dir,

                        "check_local_with_filesize_only": string_as_bool(rse_scheme["ignore_checksum"]),

                        "ignore_checksum": string_as_bool(rse_scheme["ignore_checksum"]),

                        "no_subdir": True,

                    }

lib/galaxy/tools/actions/upload.py

+1 −1
Original line number Diff line number Diff line
@@ -49,7 +49,7 @@ class RegisterToolAction(BaseUploadToolAction): 
        outputs = []

        for item in incoming.get("series", []):

            name = item.get("input", None)

            file_type = "_sniff_"

            file_type = os.path.splitext(name)[1][1:]

            dbkey = "?"

            uploaded_dataset = Bunch(type="file", name=name, file_type=file_type, dbkey=dbkey)

            tag_list = []